Yeah, there was some pretty intriguing stuff in the episode. Whatever it was Naomi was doing it didn't look to pleasant.
As for Benny, and Amelia I wouldn't be surprised if they come into play again. I'm surprised they still haven't brought up Amy in the whole Benny debate.

After seeing this episode, I fully realize the purpose of the constant flashbacks Sam and Dean have been having of their experiences of the past year other than the reveal of those experiences.

Though they reunited and went back to hunting again, I did sense that Sam and Dean haven't been completely there in the present as a team and brothers. Part of themselves have been held back by their ties to the past. Sam couldn't let go of the life he had with Amelia that was the closest he got to something normal in his life since Jessica. Dean couldn't let go of his time in Purtagory in which he discovered a bond of brotherhood with Benny that wasn't complicated by years of personal baggage like his relationship with Sam. A part of them wanted to go back to a time when things were simple and clear for them.

But what hits them this episode is that it can't happen. That if they are to hunt together again, they have to fully be there for each other as partners and brothers. That can only be accomplished by letting go of the past and embracing the present. So, at the end of the episode, we see the first step to that. Sam and Dean aren't happy about it but if they are to stop Crowley, close the doors of Hell and solve the mystery of what's going on in Heaven, this is the path they have to take. Hopefully, in time, their relationship will fully heal.